Background Familial adenomatous polyposis (FAP) is an autosomal dominantly inherited colorectal cancer predisposition caused by germ line mutations in the APC (adenomatous polyposis coli) gene. Current recommendations for APC mutation analysis advise full gene sequencing to identify point mutations and small insertions/deletions as well as the multiplex ligation dependent probe amplification (MLPA) technique to detect gene dosage alterations. Use of the protein truncation test (PTT) as a pre-screening tool has thus been largely replaced with direct end-to-end sequencing, mainly because of its limited sensitivity and failure to identify APC missense alterations.

Methods and results This report describes two unrelated patients with classical polyposis coli and unremarkable family history in whom neither full sequencing nor MLPA on leucocyte derived DNA could identify a pathogenic APC mutation. Applying the PTT, however, provided evidence of aberrant bands in both patients. Subsequent targeted mutation analysis of their tumour derived DNA allowed the identification of two novel, pathogenic APC alterations present in a mosaic state, at blood levels (1–15%) below the detection limits of conventional Sanger sequencing.

Conclusion The findings demonstrate the value of the PTT in identifying mosaic mutations in apparently APC mutation negative FAP patients with de novo classical polyposis and the need to keep the PTT within the diagnostic repertoire for APC mutation analysis.